Compiling CM-Rep

These instructions should work (with minor modifications) for MacOS and Linux. I have never tried building on Windows.

Required Packages

ITK

You will need to download and compile ITK v4.13.2. Use the following flags when compiling:

• CMAKE_CXX_FLAGS: -Wno-deprecated -std=c++11
• CMAKE_C_FLAGS: -Wno-deprecated

VTK

You will need to download and compile VTK v6.3.0. Use the following flags

• CMAKE_CXX_FLAGS: -Wno-deprecated -std=c++11
• CMAKE_C_FLAGS: -Wno-deprecated
• BUILD_SHARED_LIBS: FALSE
• VTK_REQUIRED_OBJCXX_FLAGS:

IPOPT and HSL

These constrained optimization libraries are required for compiling the newer (2013 IPMI and 2019 IPMI) programs, can be omitted for older ones.

• Download IPOPT and HSL libraries as described in https://www.coin-or.org/Ipopt/documentation/

• Recommend downloading the Full HSL package (for academic use only, must receive license)

• When compiling HSL on the Mac, I used the following configuration options. Adapt the paths to your system:

  ./configure F77=/usr/local/Cellar/gcc/4.9.2_1/bin/gfortran-4.9 FFLAGS=-fexceptions -m64 -fbackslash F90=/usr/local/Cellar/gcc/4.9.2_1/bin/gfortran-4.9 FC=/usr/local/Cellar/gcc/4.9.2_1/bin/gfortran-4.9 --prefix=/Users/pauly/tk/ipopt/install_hsl
  make
  make install
  

• When compiling HSL on recent Linux, the following suffice:

  ./configure --prefix=/home/pauly/tk/ipopt/install_hsl
  make
  make install
  

• Before compiling IPOPT, enter the ThirdParty directory and run get.XXX scripts in the directories Blas, Lapack, ASL, Mumps and Metis

• When compiling IPOPT on the Mac, I used the following command line:

  ./configure --prefix=/Users/pauly/tk/ipopt/install64_so F77=/usr/local/Cellar/gcc/4.9.2_1/bin/gfortran FFLAGS=-fexceptions -m64 -fbackslash CFLAGS=-fno-common -no-cpp-precomp -fexceptions -arch x86_64 -m64 CFLAGS=-fno-common -no-cpp-precomp -fexceptions -arch x86_64 -m64 CXXFLAGS=-fno-common -no-cpp-precomp -fexceptions -arch x86_64 -m64 --with-hsl=/Users/pauly/tk/ipopt/install_hsl/lib/libcoinhsl.a
  make
  make install
  

• For Linux:

  ./configure --prefix=/home/pauly/tk/ipopt/install --with-hsl=/home/pauly/tk/ipopt/install_hsl
  make
  make install
  

TETGEN

• Download from http://wias-berlin.de/software/tetgen/
• Build using CMake

NLOPT

This optimization library is needed for the IPMI 2019 method only * Download from https://nlopt.readthedocs.io/en/latest/ * Build using CMake

PARDISO

Sparse solver, needed for PDE-based cm-rep programs (2005 IPMI, 2008 NeuroImage) * Download from https://www.pardiso-project.org/ * Get license and follow instructions for how to use it * The easiest is to put the library into /usr/local/lib

Building CM-Rep

• Create a build directory and run ccmake there
• Set the following flags to ON:
  • USE_IPOPT (recommended, use for 2013 and 2019 boundary-first methods)
  • USE_HSL (recommended, use for 2013 and 2019 boundary-first methods)
  • USE_TETGEN
  • USE_NLOPT (recommended, use for 2019 boundary-first method)
  • USE_PARDISO (optional, use for 2006 and 2008 PDE-based method)
• Set the necessary library and include paths:
  • ITK_DIR (point to ITK build directory)
  • VTK_DIR (point to VTK build directory)
  • IPOPT_LIBRARY (e.g., /home/pauly/tk/ipopt/install/lib/libipopt.so)
  • IPOPT_INCLUDE_DIR (e.g., /home/pauly/tk/ipopt/install/include/coin)
  • IPOPT_HSL_LIBRARY (e.g., /home/pauly/tk/ipopt/install_hsl/libcoinhsl.so)
  • IPOPT_GFORTRAN_LIB (point to system gfortran, e.g., /usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortran.so)
  • IPOPT_BLAS_LIB (point to BLAS, e.g., /home/pauly/tk/ipopt/install/lib/libcoinblas.so)
  • TETGEN_LIBRARY: (e.g., /home/pauly/tk/tetgen/build/libtet.a)
  • TETGEN_INCLUDE_DIR: (e.g., /home/pauly/tk/tetgen)
  • NLOPT_LIBRARIES: (e.g., /home/pauly/tk/nlopt/build/lib/libnlopt.so)
  • NLOPT_INCLUDE_DIRS: (e.g., /home/pauly/tk/nlopt/include)
• When using PARDISO:
  • PARDISO_LIB (point to the shared library)
  • LAPACK_LIB (point to the system Lapack)
  • GOMP_LIB (point to the system GOMP: GNU OpenMP library)
• Set compilation flags:
  • CMAKE_CXX_FLAGS: set to match those for ITK/VTK, i.e., -Wno-deprecated -std=c++11
  • CMAKE_C_FLAGS: set to match those for ITK/VTK, i.e., -Wno-deprecated
• Run make